DISTING: A web application for fast algorithmic computation of alternative indistinguishable linear compartmental models.

BACKGROUND AND OBJECTIVES: We describe and illustrate use of DISTING, a novel web application for computing alternative structurally identifiable linear compartmental models that are input-output indistinguishable from a postulated linear compartmental model. Several computer packages are available for analysing the structural identifiability of such models, but DISTING is the first to be made available for assessing indistinguishability. METHODS: The computational algorithms embedded in DISTING are based on advanced versions of established geometric and algebraic properties of linear compartmental models, embedded in a user-friendly graphic model user interface. Novel computational tools greatly speed up the overall procedure. These include algorithms for Jacobian matrix reduction, submatrix rank reduction, and parallelization of candidate rank computations in symbolic matrix analysis. RESULTS: The application of DISTING to three postulated models with respectively two, three and four compartments is given. The 2-compartment example is used to illustrate the indistinguishability problem; the original (unidentifiable) model is found to have two structurally identifiable models that are indistinguishable from it. The 3-compartment example has three structurally identifiable indistinguishable models. It is found from DISTING that the four-compartment example has five structurally identifiable models indistinguishable from the original postulated model. This example shows that care is needed when dealing with models that have two or more compartments which are neither perturbed nor observed, because the numbering of these compartments may be arbitrary. CONCLUSIONS: DISTING is universally and freely available via the Internet. It is easy to use and circumvents tedious and complicated algebraic analysis previously done by hand.

Analysis of amino acid residues in the predicted transmembrane pore influencing transport kinetics of the hepatic drug transporter organic anion transporting polypeptide 1B1 (OATP1B1).

The hepatic uptake transporters OATP1B1 (SLCO1B1) and OATP1B3 (SLCO1B3) mediate the uptake of endogenous metabolites and drugs from blood into hepatocytes. Alterations of transport function are accompanied with variations in drug plasma concentrations and the risk of adverse drug effects. Thus, knowledge on amino acids determining substrate recognition or transport kinetics are important to predict alterations in transport kinetics. Therefore, we analyzed the charged amino acids His54 and Tyr169, both located at the extracellular entry of the predicted transmembrane pore of OATP1B1. Based on a computational analysis we established HEK293 cell lines overexpressing the mutant OATP1B1 proteins HEK-OATP1B1p.H54Q, -p.H54A, -p.Y169H and -p.Y169A and analyzed protein expression, localization and transport kinetics of the four OATP1B1 substrates bromosulfophthalein, estradiaol-17ß-glucuronide, taurocholate and pravastatin. Consequences on transport were detected for all mutants and these were different for each amino acid exchange and for each substrate tested. For example, the exchange H54Q resulted in reduced transport for BSP (78% of wildtype OATP1B1 transport at 0.05µM, P<0.01) with reduced affinity to this substrate (Km value increases from 0.76µM to 8.04µM) but in stimulated E217ßG transport (138% compared to wildtype transport at 10µM, P<0.001). Investigating amino acid exchanges located at the extracellular entry of the transport pore of the OATP1B1 protein we demonstrated that these residues are involved in modulating transport kinetics and this participation strongly depends on the substrate and not on the physicochemical character of the investigated amino acid.

Near­infrared fluorescence imaging of prostate cancer using heptamethine carbocyanine dyes.

Near­infrared fluorescence (NIRF) imaging is an attractive novel modality for the detection of cancer. A previous study defined two organic polymethine cyanine dyes as ideal NIRF probes, IR­783 and its derivative MHI­148, which have excellent optical characteristics, superior biocompatibility and cancer targeting abilities. To investigate the feasibility of NIRF dye­mediated prostate cancer imaging, dye uptake and subcellular co­localization were investigated in PC­3, DU­145 and LNCaP human prostate cancer cells and RWPE­1 normal prostate epithelial cells. Different organic anion transporting peptide (OATP) inhibitors were utilized to explore the potential role of the OATP subtype, including the nonspecific OATP inhibitor bromosulfophthalein, the OATP1 inhibitor 17ß­estradiol, the selective OATP1B1 inhibitor rifampicin and the selective OATP1B3 inhibitor cholecystokinin octapeptide. NIRF dyes were also used for the simulated detection of circulating tumor cells and the rapid detection of prostate cancer in human prostate cancer tissues and prostate cancer xenografts in mouse models. The results revealed that the cancer­specific uptake of these organic dyes in prostate cancer cells occurred primarily via OATP1B3. A strong NIRF signal was detected in prostate cancer tissues, but not in normal tissues that were stained with IR­783. Prostate cancer cells were recognized with particular NIR fluorescence in isolated mononuclear cell mixtures. The results of the present study demonstrated that NIRF dye­mediated imaging is a feasible and practicable method for prostate cancer detection, although further investigative studies are required before clinical translation.

Fluorescence study on the interaction of human serum albumin with bromsulphalein.

The binding of bromsulphalein (BSP) with human serum albumin was investigated at different temperatures, 298 and 308 K, by the fluorescence spectroscopy at pH 7.24. The binding constant was determined by Stern-Volmer equation based on the quenching of the fluorescence HSA in the presence of bromsulphalein. The effect of various metal ions on the binding constants of BSP with HSA was investigated. The thermodynamic parameters were calculated according to the dependence of enthalpy change on the temperature as follows: DeltaH and DeltaS possess small negative (9.3 kJ mol(-1)) and positive values (22.3 J K(-l)mol(-l)), respectively. The experimental results revealed that BSP has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. The binding constants between BSP to HSA were remarkable and independent on temperature. The binding constants between HSA and BSP decreased in the presence of various ions, commonly decreased by 30-55%. The hydrophobic force played a major role in the interaction of BSP with HSA. All these experimental results and theoretical data clarified that BSP could bind to HSA and be effectively transported and eliminated in body, which could be a useful guideline for further drug design.

Interaction with PDZK1 is required for expression of organic anion transporting protein 1A1 on the hepatocyte surface.

Although many organic anion transport protein (Oatp) family members have PDZ consensus binding sites at their C termini, the functional significance is unknown. In the present study, we utilized rat Oatp1a1 (NM_017111) as a prototypical member of this family to examine the mechanism governing its subcellular trafficking. A peptide corresponding to the C-terminal 16 amino acids of rat Oatp1a1 was used to affinity-isolate interacting proteins from rat liver cytosol. Protein mass fingerprinting identified PDZK1 as the major interacting protein. This was confirmed by immunoprecipitation of an Oatp1a1-PDZK1 complex from cotransfected 293T cells as well as from native rat liver membrane extracts. Oatp1a1 bound predominantly to the first and third PDZ binding domains of PDZK1, whereas the high density lipoprotein receptor, scavenger receptor B type I binds to the first domain. Although it is possible that PDZK1 forms a complex with these two integral membrane proteins, this did not occur, suggesting that as yet undescribed factors lead to selectivity in the interaction of these protein ligands with PDZK1. Oatp1a1 protein expression was near normal in PDZK1 knock-out mouse liver. However, it was located predominantly in intracellular structures, in contrast to its normal basolateral plasma membrane distribution. Plasma disappearance of the Oatp1a1 ligand [35S]sulfobromophthalein was correspondingly delayed in knock-out mice. These studies show a critical role for oligomerization of Oatp1a1 with PDZK1 for its proper subcellular localization and function. Because its ability to transport substances into the cell requires surface expression, this must be considered in any assessment of physiologic function.

Characterization of bromosulphophthalein binding to human glutathione S-transferase A1-1: thermodynamics and inhibition kinetics.

In addition to their catalytic functions, GSTs (glutathione S-transferases) bind a wide variety of structurally diverse non-substrate ligands. This ligandin function is known to result in the inhibition of catalytic function. The interaction between hGSTA1-1 (human class Alpha GST with two type 1 subunits) and a non-substrate anionic ligand, BSP (bromosulphophthalein), was studied by isothermal titration calorimetry and inhibition kinetics. The binding isotherm is biphasic, best described by a set of two independent sites: a high-affinity site and a low-affinity site(s). The binding stoichiometries for these sites are 1 and 3 molecules of BSP respectively. BSP binds to the high-affinity site 80 times more tightly (K(d)=0.12 microM) than it does to the low-affinity site(s) (K(d)=9.1 microM). Binding at these sites is enthalpically and entropically favourable, with no linkage to protonation events. Temperature- and salt-dependent studies indicate the significance of hydrophobic interactions in the binding of BSP, and that the low-affinity site(s) displays low specificity towards the anion. Binding of BSP results in the release of ordered water molecules at these hydrophobic sites, which more than offsets unfavourable entropic changes during binding. BSP inhibition studies show that the binding of BSP to its high-affinity site does not inhibit hGSTA1-1. This site, located near Trp-20, may be related to the buffer-binding site observed in GSTP1-1. The low-affinity-binding site(s) for BSP is most probably located at or near the active site of hGSTA1-1. Binding to this site(s) results in non-competitive inhibition with respect to CDNB (1-chloro-2,4-dinitrobenzene) (K(i)(BSP)=16.8+/-1.9 microM). Given the properties of the H site and the relatively small size of the electrophilic substrate CDNB, it is plausible that the active site of the enzyme can simultaneously accommodate both BSP and CDNB. This would explain the non-competitive behaviour of certain inhibitors that bind the active site (e.g. BSP).

Metabolism of sulphobromophthalein I: positional isomers of sulphobromophthalein monoglutathione conjugate.

Three positional isomers of sulphobromophthalein glutathione monoconjugate (BSP-mGSH) were detected using a paired-ion HPLC method that employs triethylamine phosphate (TEA-H3PO4) as a pairing agent. To confirm that these compounds were glutathione (GSH) conjugates, sulphobromophthalein (BSP) was incubated with a four-fold volume of GSH under alkaline ammonium hydroxide. At least 6 metabolites (3 di-GSH conjugates and 3 isomers of mono-GSH conjugates) were produced under these conditions. The three mono-GSH conjugates were each purified and identified as compounds with a molecular weight of 1,020 according to FAB mass spectrometry results. Positional isomers of BSP-GSH were provisionally distinguished via the addition of the symbols alpha, beta and delta to the end of each abbreviation, to reflect the amount of isomers present. Thus, the isomer present in the largest quantity was termed BSP-mGSH(alpha), the second most abundant isomer was termed BSP-mGSH(beta) and the third was termed BSP-mGSH(delta). Interestingly, a species difference was recognized in that rat cytosol GSH S-transferase (GST) primarily produced BSP-mGSH(alpha), whereas guinea-pig cytosol generated BSP-mGSH(delta), BSP-mGSH(alpha) and BSP-mGSH(beta) equally and rabbit cytosol mainly produced BSP-mGSH(beta).

Extensions to a procedure for generating locally identifiable reparameterisations of unidentifiable systems.

In this paper extensions to an existing procedure for generating locally identifiable reparameterisations of unidentifiable systems are presented. These extensions further formalise the constructive nature of the methodology and lend themselves to application within symbolic manipulation packages. The extended reparameterisation procedure is described in detail and is illustrated with application to two known non-trivial examples of unidentifiable systems of practical relevance.

The ligandin (non-substrate) binding site of human Pi class glutathione transferase is located in the electrophile binding site (H-site).

Glutathione S -transferases (GSTs) play a pivotal role in the detoxification of foreign chemicals and toxic metabolites. They were originally termed ligandins because of their ability to bind large molecules (molecular masses >400 Da), possibly for storage and transport roles. The location of the ligandin site in mammalian GSTs is still uncertain despite numerous studies in recent years. Here we show by X-ray crystallography that the ligandin binding site in human pi class GST P1-1 occupies part of one of the substrate binding sites. This work has been extended to the determination of a number of enzyme complex crystal structures which show that very large ligands are readily accommodated into this substrate binding site and in all, but one case, causes no significant movement of protein side-chains. Some of these molecules make use of a hitherto undescribed binding site located in a surface pocket of the enzyme. This site is conserved in most, but not all, classes of GSTs suggesting it may play an important functional role.

Glutathione analogues as novel inhibitors of rat and human glutathione S-transferase isoenzymes, as well as of glutathione conjugation in isolated rat hepatocytes and in the rat in vivo.

Inhibitors of rat and human Alpha- and Mu-class glutathione S-transferases that effectively inhibit the glutathione (GSH) conjugation of bromosulphophthalein in the rat liver cytosolic fraction, isolated rat hepatocytes and in the rat liver in vivo have been developed. The GSH analogue (R)-5-carboxy-2-gamma-(S)-glutamylamino-N-hexylpentamide [Adang, Brussee, van der Gen and Mulder (1991) J. Biol. Chem. 266, 830-836] was used as the lead compound. To obtain more potent inhibitors, it was modified by replacement of the N-hexyl moiety by N-2-heptyl and by esterification of the 5-carboxy group with ethyl and dodecyl groups. In isolated hepatocytes, the branched N-2-heptyl derivatives were stronger inhibitors of GSH conjugation of bromosulphophthalein than the N-hexyl derivatives. The ethyl ester compounds were more efficient than the corresponding unesterified derivatives. The dodecyl ester of the N-2-heptyl analogue was the most effective inhibitor in isolated hepatocytes, but was relatively toxic in vivo. However, the corresponding ethyl ester was a potent in vivo inhibitor: GSH conjugation of bromosulphophthalein (as assessed by biliary excretion of the conjugate) was decreased by 70% after administration of a dose of 200 mumol/kg. The isoenzyme specificity of the inhibitors towards purified rat and human glutathione S-transferases was also examined. The unesterified compounds were more potent than the esterified analogues, and inhibited Alpha- and Mu-class isoenzymes of both rat and human glutathione S-transferase (Ki range 1-40 microM). Other GSH-dependent enzymes, i.e. GSH peroxidase, GSH reductase and gamma-glutamyltranspeptide, were not inhibited. Thus (R)-5-ethyloxycarbonyl-2-gamma-(S)-glutamylamino-N-2-hept ylpentamide, the in vivo inhibitor of GSH conjugation, may be useful in helping to assess the role of the Alpha and Mu classes of glutathione S-transferases in cellular biochemistry, physiology and pathology.

Porcine class pi glutathione S-transferase: anionic ligand binding and conformational analysis.

The equilibrium binding of the non-substrate ligands 8-anilino-1-naphthalene sulfonate and bromosulfophthalein to porcine class pi glutathione S-transferase (pGSTP1-1) was studied using a variety of techniques (size-exclusion HPLC, steady-state fluorescence, second-derivative spectroscopy, and chemical modification of cysteines). Both ligands share the same binding site which has a highly hydrophobic surface. Occupation of the site inhibits catalytic function with glutathione and 1-chloro-2,4-dinitrobenzene in a non-competitive manner. Data obtained from different structural probes either located at strategic regions of pGSTP1-1 (Trp-28, Trp-38 and Cys-45) or distributed throughout the protein molecule (tyrosine residues) suggest that binding induces a microstructural change that impacts on the functional conformation of the active site.

Difference in hepatic uptake of tetra- and di-bromosulfophthalein in rat. Role of hydrophobicity, binding to plasma proteins and affinity for plasma membrane carrier protein.

The relative role of hydrophobicity, binding to plasma proteins and affinity for one of the plasma membrane transport proteins in the hepatic uptake of 3,4,5,6-tetra- (BSP) and 3,6-di- (DBSP) bromosulfophthalein was investigated in the rat. In terms of physicochemical characteristics, the two molecules show different pKa values and degrees of hydrophobicity, as determined from the n-octanol:water partition coefficient. In the intact animal, the plasma clearance and the plasma removal rate after a dose of 1.5 mumol/kg i.v. were significantly (P < 0.001) faster for BSP than DBSP, while no difference was found in the plasma distribution volume. The dissociation constant (Kd) of the high affinity binding sites of plasma proteins also differed for the two anions, being significantly lower for BSP than DBSP (0.95 +/- 0.02 vs 1.44 +/- 0.14 microM, P < 0.001). [35S]BSP uptake by liver plasma membrane vesicles was saturable with an apparent Km of 5.20 +/- 0.80 microM, and was competitively inhibited by DBSP (Ki 18.2 +/- 1.2 microM) indicating a common uptake system. The Kd value for binding of the organic anions to purified bilitranslocase, a plasma membrane protein involved in the electrogenic transport of pthaleins, was also significantly lower for BSP than DBSP (1.10 +/- 0.12 vs 3.02 +/- 0.27 microM, N = 3, P < 0.001), indicating a higher affinity of the former ligand for the carrier protein. No difference was observed in the capacity of the high affinity binding sites (32 +/- 3 vs 33 +/- 3 nmol/mg protein, BSP and DBSP, respectively). These data indicate that BSP and DBSP are two different cholephilic organic anions which share a common uptake mechanism, at least partly mediated by bilitranslocase. The greater affinity of BSP than DBSP for the carrier protein may account for the faster plasma disappearance rate of BSP observed in vivo, in spite of the higher plasma protein binding.

Design of two chimaeric human-rat class alpha glutathione transferases for probing the contribution of C-terminal segments of protein structure to the catalytic properties.

Two chimaeric human-rat class Alpha glutathione transferases were constructed by fusion of DNA segments derived from the plasmids pTGT2-AT and pGTB38 and expression of the corresponding proteins in Escherichia coli. The recombinant proteins H1R1/1 and H1R1/2 encoded by plasmids pH1R1/1 and pH1R1/2 are composed of a segment of the human class Alpha subunit 1 from the N-terminus to His-143 and Pro-207 respectively, followed by the complementary C-terminal portion of the rat class Alpha subunit 1 sequence. Compared with the parental human enzyme, H1R1/1 is altered in 20 positions due to the introduction of 79 residues from the rat enzyme, while H1R1/2 is altered in five positions out of 15 in the C-terminal region. The design of mutant H1R1/1 is equivalent to introduction of exons 6 and 7 of the rat subunit 1 gene in place of the homologous human nucleotide sequence. The two chimaeric proteins are enzymatically active with several substrates, even though the activity in most cases is somewhat decreased in comparison with the wild-type human enzyme. Inhibition studies show that the kinetic properties mimic those of the human enzyme, indicating that the N-terminal two-thirds of the primary structure plays the major role in governing the catalytic properties. The results of this study demonstrate that recombination of segments of primary structure between homologous enzymes may serve as a useful cassette technique for design of novel catalytically active proteins.